Pub Date : 2023-12-03DOI: 10.3390/biophysica3040044
Bojin Chen, J. Z. Zhang
Serine hydroxymethyltransferase 2 (SHMT2) has garnered significant attention as a critical catalytic regulator of the serine/glycine pathway in the one-carbon metabolism of cancer cells. Despite its potential as an anti-cancer target, only a limited number of inhibitors have been identified so far. In this study, we employed seven different scoring functions and skeleton clustering to screen the ChemDiv database for 38 compounds, 20 of which originate from the same skeleton structure. The most significant residues from SHMT2 and chemical groups from the inhibitors were identified using ASGBIE (Alanine Scanning with Generalized Born model and Interaction Entropy), and the binding energy of each residue was quantitatively determined, revealing the essential features of the protein–inhibitor interaction. The two most important contributing residues are TYR105 and TYR106 of the B chain followed by LEU166 and ARG425 of the A chain. The findings will be greatly helpful in developing a thorough comprehension of the binding mechanisms involved in drug–SHMT2 interactions and offer valuable direction for designing more potent inhibitors.
丝氨酸羟甲基转移酶2 (SHMT2)作为癌细胞单碳代谢中丝氨酸/甘氨酸通路的关键催化调节剂，引起了人们的广泛关注。尽管它具有抗癌靶点的潜力，但到目前为止，只有有限数量的抑制剂被发现。在这项研究中，我们使用了7种不同的评分函数和骨架聚类来筛选ChemDiv数据库中的38个化合物，其中20个化合物来自相同的骨架结构。利用ASGBIE (Alanine Scanning with Generalized Born model and Interaction Entropy)对抑制剂中最显著的SHMT2残基和化学基团进行了鉴定，并定量测定了每个残基的结合能，揭示了蛋白-抑制剂相互作用的基本特征。两个最重要的贡献残基是B链的TYR105和TYR106，其次是A链的LEU166和ARG425。这些发现将极大地有助于深入了解药物- shmt2相互作用的结合机制，并为设计更有效的抑制剂提供有价值的指导。
{"title":"Screening and Analysis of Potential Inhibitors of SHMT2","authors":"Bojin Chen, J. Z. Zhang","doi":"10.3390/biophysica3040044","DOIUrl":"https://doi.org/10.3390/biophysica3040044","url":null,"abstract":"Serine hydroxymethyltransferase 2 (SHMT2) has garnered significant attention as a critical catalytic regulator of the serine/glycine pathway in the one-carbon metabolism of cancer cells. Despite its potential as an anti-cancer target, only a limited number of inhibitors have been identified so far. In this study, we employed seven different scoring functions and skeleton clustering to screen the ChemDiv database for 38 compounds, 20 of which originate from the same skeleton structure. The most significant residues from SHMT2 and chemical groups from the inhibitors were identified using ASGBIE (Alanine Scanning with Generalized Born model and Interaction Entropy), and the binding energy of each residue was quantitatively determined, revealing the essential features of the protein–inhibitor interaction. The two most important contributing residues are TYR105 and TYR106 of the B chain followed by LEU166 and ARG425 of the A chain. The findings will be greatly helpful in developing a thorough comprehension of the binding mechanisms involved in drug–SHMT2 interactions and offer valuable direction for designing more potent inhibitors.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"55 17","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138604896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-25DOI: 10.3390/biophysica3040043
Maurizio Sabbatini, Valentina Bonetto, Valeria Magnelli, C. Lorusso, Francesco Dondero, Maria Angela Masini
Gravity is a primary physical force that has a profound influence on the stability of the cell cytoskeleton. In our research, we investigated the influence of microgravity on altering the cytoskeletal pathways of glioblastoma cells. The highly infiltrative behavior of glioblastoma is supported by cytoskeletal dynamics and surface proteins that allow glioblastoma cells to avoid stable connections with the tissue environment and other cells. Glioblastoma cell line C6 was exposed to a microgravity environment for 24, 48, and 72 h by 3D-RPM, a laboratory instrument recognized to reproduce the effect of microgravity in cell cultures. The immunofluorescence for GFAP, vinculin, and Connexin-43 was investigated as signals related to cytoskeleton dynamics. The polymerization of GFAP and the expression of focal contact structured by vinculin were found to be altered, especially after 48 and 72 h of microgravity. Connexin-43, involved in several intracellular pathways that critically promote cell motility and invasion of glioma cells, was found to be largely reduced following microgravity exposure. In conclusion, microgravity, by reducing the expression of Connexin-43, alters the architecture of specific cytoskeletal elements such as GFAP and increases the focal contact, which can induce a reduction in glioma cell mobility, thereby inhibiting their aggressive metastatic behavior.
{"title":"Microgravity as an Anti-Metastatic Agent in an In Vitro Glioma Model","authors":"Maurizio Sabbatini, Valentina Bonetto, Valeria Magnelli, C. Lorusso, Francesco Dondero, Maria Angela Masini","doi":"10.3390/biophysica3040043","DOIUrl":"https://doi.org/10.3390/biophysica3040043","url":null,"abstract":"Gravity is a primary physical force that has a profound influence on the stability of the cell cytoskeleton. In our research, we investigated the influence of microgravity on altering the cytoskeletal pathways of glioblastoma cells. The highly infiltrative behavior of glioblastoma is supported by cytoskeletal dynamics and surface proteins that allow glioblastoma cells to avoid stable connections with the tissue environment and other cells. Glioblastoma cell line C6 was exposed to a microgravity environment for 24, 48, and 72 h by 3D-RPM, a laboratory instrument recognized to reproduce the effect of microgravity in cell cultures. The immunofluorescence for GFAP, vinculin, and Connexin-43 was investigated as signals related to cytoskeleton dynamics. The polymerization of GFAP and the expression of focal contact structured by vinculin were found to be altered, especially after 48 and 72 h of microgravity. Connexin-43, involved in several intracellular pathways that critically promote cell motility and invasion of glioma cells, was found to be largely reduced following microgravity exposure. In conclusion, microgravity, by reducing the expression of Connexin-43, alters the architecture of specific cytoskeletal elements such as GFAP and increases the focal contact, which can induce a reduction in glioma cell mobility, thereby inhibiting their aggressive metastatic behavior.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139238322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-11DOI: 10.3390/biophysica3040042
Bashiyar Almarwani, Yahia Z. Hamada, Nsoki Phambu, Anderson Sunda-Meya
The cell-penetrating peptide (CPP) penetratin (PEN) has garnered attention for its potential to enter tumor cells. However, its translocation mechanism and lack of selectivity remain debated. This study investigated PEN’s insertion into healthy cells (H-) and cancer cells (C-) using micromolar concentrations and various techniques. Raman spectroscopy was used to determine PEN’s location in the lipid bilayer at different lipid-to-peptide ratios. Dynamic light scattering (DLS) and zeta potential analysis were used to measure the lipid–PEN complex’s size and charge. The results showed helical PEN particles directly inserted into C- membranes at a ratio of 110, while aggregated particles stayed on H- surfaces. Raman spectroscopy and scanning electron microscopy confirmed PEN insertion in C- membranes. Zeta potential studies revealed highly negative charges for PEN–C- complexes and neutral charges for PEN–H- complexes at pH 6.8. C- integrity remained unchanged at a ratio of 110. Specific lipid-to-peptide ratios with dipalmitoylphosphatidylserine (DPPS) were crucial for direct insertion. These results provide valuable insights into CPP efficacy for targeted drug delivery in cancer cells, considering membrane composition and lipid-to-peptide ratios.
{"title":"Investigating the Insertion Mechanism of Cell-Penetrating Peptide Penetratin into Cell Membranes: Implications for Targeted Drug Delivery","authors":"Bashiyar Almarwani, Yahia Z. Hamada, Nsoki Phambu, Anderson Sunda-Meya","doi":"10.3390/biophysica3040042","DOIUrl":"https://doi.org/10.3390/biophysica3040042","url":null,"abstract":"The cell-penetrating peptide (CPP) penetratin (PEN) has garnered attention for its potential to enter tumor cells. However, its translocation mechanism and lack of selectivity remain debated. This study investigated PEN’s insertion into healthy cells (H-) and cancer cells (C-) using micromolar concentrations and various techniques. Raman spectroscopy was used to determine PEN’s location in the lipid bilayer at different lipid-to-peptide ratios. Dynamic light scattering (DLS) and zeta potential analysis were used to measure the lipid–PEN complex’s size and charge. The results showed helical PEN particles directly inserted into C- membranes at a ratio of 110, while aggregated particles stayed on H- surfaces. Raman spectroscopy and scanning electron microscopy confirmed PEN insertion in C- membranes. Zeta potential studies revealed highly negative charges for PEN–C- complexes and neutral charges for PEN–H- complexes at pH 6.8. C- integrity remained unchanged at a ratio of 110. Specific lipid-to-peptide ratios with dipalmitoylphosphatidylserine (DPPS) were crucial for direct insertion. These results provide valuable insights into CPP efficacy for targeted drug delivery in cancer cells, considering membrane composition and lipid-to-peptide ratios.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"39 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135086874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-31DOI: 10.3390/biophysica3040041
David Reguera, Pedro J. de Pablo, Nicola G. A. Abrescia, Mauricio G. Mateu, Javier Hernández-Rojas, José R. Castón, Carmen San Martín
Virus particles consist of a protein coat that protects their genetic material and delivers it to the host cell for self-replication. Understanding the interplay between virus structure and function is a requirement for understanding critical processes in the infectious cycle such as entry, uncoating, genome metabolism, capsid assembly, maturation, and propagation. Together with well-established techniques in cell and molecular biology, physical virology has emerged as a rapidly developing field, providing detailed, novel information on the basic principles of virus assembly, disassembly, and dynamics. The Spanish research community contains a good number of groups that apply their knowledge on biology, physics, or chemistry to the study of viruses. Some of these groups got together in 2010 under the umbrella of the Spanish Interdisciplinary Network on Virus Biophysics (BioFiViNet). Thirteen years later, the network remains a fertile ground for interdisciplinary collaborations geared to reveal new aspects on the physical properties of virus particles, their role in regulating the infectious cycle, and their exploitation for the development of virus-based nanotechnology tools. Here, we highlight some achievements of Spanish groups in the field of physical virology.
{"title":"Physical Virology in Spain","authors":"David Reguera, Pedro J. de Pablo, Nicola G. A. Abrescia, Mauricio G. Mateu, Javier Hernández-Rojas, José R. Castón, Carmen San Martín","doi":"10.3390/biophysica3040041","DOIUrl":"https://doi.org/10.3390/biophysica3040041","url":null,"abstract":"Virus particles consist of a protein coat that protects their genetic material and delivers it to the host cell for self-replication. Understanding the interplay between virus structure and function is a requirement for understanding critical processes in the infectious cycle such as entry, uncoating, genome metabolism, capsid assembly, maturation, and propagation. Together with well-established techniques in cell and molecular biology, physical virology has emerged as a rapidly developing field, providing detailed, novel information on the basic principles of virus assembly, disassembly, and dynamics. The Spanish research community contains a good number of groups that apply their knowledge on biology, physics, or chemistry to the study of viruses. Some of these groups got together in 2010 under the umbrella of the Spanish Interdisciplinary Network on Virus Biophysics (BioFiViNet). Thirteen years later, the network remains a fertile ground for interdisciplinary collaborations geared to reveal new aspects on the physical properties of virus particles, their role in regulating the infectious cycle, and their exploitation for the development of virus-based nanotechnology tools. Here, we highlight some achievements of Spanish groups in the field of physical virology.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"37 3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135870248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-28DOI: 10.3390/biophysica3040040
Yasith Indigahawela Gamage, Jianjun Pan
Understanding the membrane interactions of the N-terminal 17 residues of the huntingtin protein (HttN) is essential for unraveling its role in cellular processes and its impact on huntingtin misfolding. In this study, we used atomic force microscopy (AFM) to examine the effects of lipid specificity in mediating bilayer perturbations induced by HttN. Across various lipid environments, the peptide consistently induced bilayer disruptions in the form of holes. Notably, our results unveiled that cholesterol enhanced bilayer perturbation induced by HttN, while phosphatidylethanolamine (PE) lipids suppressed hole formation. Furthermore, anionic phosphatidylglycerol (PG) and cardiolipin lipids, along with cholesterol at high concentrations, promoted the formation of double-bilayer patches. This unique structure suggests that the synergy among HttN, anionic lipids, and cholesterol can enhance bilayer fusion, potentially by facilitating lipid intermixing between adjacent bilayers. Additionally, our AFM-based force spectroscopy revealed that HttN enhanced the mechanical stability of lipid bilayers, as evidenced by an elevated bilayer puncture force. These findings illuminate the complex interplay between HttN and lipid membranes and provide useful insights into the role of lipid composition in modulating membrane interactions with the huntingtin protein.
{"title":"Elucidating the Influence of Lipid Composition on Bilayer Perturbations Induced by the N-Terminal Region of the Huntingtin Protein","authors":"Yasith Indigahawela Gamage, Jianjun Pan","doi":"10.3390/biophysica3040040","DOIUrl":"https://doi.org/10.3390/biophysica3040040","url":null,"abstract":"Understanding the membrane interactions of the N-terminal 17 residues of the huntingtin protein (HttN) is essential for unraveling its role in cellular processes and its impact on huntingtin misfolding. In this study, we used atomic force microscopy (AFM) to examine the effects of lipid specificity in mediating bilayer perturbations induced by HttN. Across various lipid environments, the peptide consistently induced bilayer disruptions in the form of holes. Notably, our results unveiled that cholesterol enhanced bilayer perturbation induced by HttN, while phosphatidylethanolamine (PE) lipids suppressed hole formation. Furthermore, anionic phosphatidylglycerol (PG) and cardiolipin lipids, along with cholesterol at high concentrations, promoted the formation of double-bilayer patches. This unique structure suggests that the synergy among HttN, anionic lipids, and cholesterol can enhance bilayer fusion, potentially by facilitating lipid intermixing between adjacent bilayers. Additionally, our AFM-based force spectroscopy revealed that HttN enhanced the mechanical stability of lipid bilayers, as evidenced by an elevated bilayer puncture force. These findings illuminate the complex interplay between HttN and lipid membranes and provide useful insights into the role of lipid composition in modulating membrane interactions with the huntingtin protein.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136232004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-26DOI: 10.3390/biophysica3040039
Ishmael Apachigawo, Dhruvil Solanki, Ruth Tate, Himanshi Singh, Mohammad Moshahid Khan, Prabhakar Pradhan
Biological tissues in nature are fractal due to their self-similarity and porosity properties. These properties change with the progress of some diseases, including brain tissue in leading neurological disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Thus, there is an unmet clinical need to develop a tool for accurate and early diagnosis of AD and PD conditions. Although the whole brain tissues in AD and PD have been extensively studied, their local structural alterations at the nano-to-submicron levels have not been explored. In this paper, we measure the local structural alterations in different brain regions of AD and PD patients by measuring their change in fractal dimensions via optical microscopy. Our results show an increase in the fractal dimension value of ~5–10% in the affected regions of the brain tissues relative to their respective controls. For AD cases, the structural alteration is attributed to the aberrant deposition of amyloid beta protein and neurofibrillary tangles in the brain, and for PD, the gradual loss of dopaminergic neurons and abnormal accumulation of α-synuclein in the brain. The work will enhance the further understanding of alterations in the brain structures in AD and PD and its detection.
{"title":"Fractal Dimension Analyses to Detect Alzheimer’s and Parkinson’s Diseases Using Their Thin Brain Tissue Samples via Transmission Optical Microscopy","authors":"Ishmael Apachigawo, Dhruvil Solanki, Ruth Tate, Himanshi Singh, Mohammad Moshahid Khan, Prabhakar Pradhan","doi":"10.3390/biophysica3040039","DOIUrl":"https://doi.org/10.3390/biophysica3040039","url":null,"abstract":"Biological tissues in nature are fractal due to their self-similarity and porosity properties. These properties change with the progress of some diseases, including brain tissue in leading neurological disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Thus, there is an unmet clinical need to develop a tool for accurate and early diagnosis of AD and PD conditions. Although the whole brain tissues in AD and PD have been extensively studied, their local structural alterations at the nano-to-submicron levels have not been explored. In this paper, we measure the local structural alterations in different brain regions of AD and PD patients by measuring their change in fractal dimensions via optical microscopy. Our results show an increase in the fractal dimension value of ~5–10% in the affected regions of the brain tissues relative to their respective controls. For AD cases, the structural alteration is attributed to the aberrant deposition of amyloid beta protein and neurofibrillary tangles in the brain, and for PD, the gradual loss of dopaminergic neurons and abnormal accumulation of α-synuclein in the brain. The work will enhance the further understanding of alterations in the brain structures in AD and PD and its detection.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"111 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134908793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-27DOI: 10.3390/biophysica3040038
James P. Chambers, Elena T. Wright, Barbara Hunter, Philip Serwer
Phage characterization for research and therapy can involve newly isolated phages propagated in pathogenic bacteria. If so, characterization requires safety-managing the bacteria. In the current study, we adapt a common and inexpensive reagent, PrimeStore (Longhorn Vaccines and Diagnostics, San Antonio, TX, USA), to safety-manage bacteria in 20 min by selectively inactivating the bacteria. No bacterial survivors are observed among >109 bacteria per ml for a representative of both Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Bacillus thuringiensis). This procedure causes no detected inactivation of podophage T3, myophage T4 and siphophage 0105phi7-2. Margins of safety for PrimeStore concentration exist for bacterial inactivation and phage non-inactivation. Thus, general applicability is expected. Subsequent dialysis is used to block long-term effects on phages. Nonetheless, comparable tests should be performed for each pathogenic bacterial strain/phage. Electron microscopy of thin sections reveals inactivation-altered bacterial cytoplasm and a non-disintegrated bacterial envelope (ghosts). Ghosting of E. coli includes re-arrangement of the cytoplasm and the release of endotoxin. The activity of the released endotoxin is >99% reduced after subsequent dialysis, which also removes PrimeStore components. Ghosting of B. thuringiensis includes apparent phase separation within the cytoplasm. The primary application envisaged is biophysical and other screening of phages for therapy of infectious disease.
用于研究和治疗的噬菌体表征可涉及在致病菌中繁殖的新分离噬菌体。如果是这样的话，表征就需要对细菌进行安全管理。在目前的研究中，我们采用了一种常见且廉价的试剂PrimeStore (Longhorn Vaccines and Diagnostics, San Antonio, TX, USA)，通过选择性灭活细菌，在20分钟内对细菌进行安全管理。在每毫升109个革兰氏阴性菌(大肠杆菌)和革兰氏阳性菌(苏云金芽孢杆菌)中均未观察到细菌存活。该过程未检测到足噬细胞T3、肌噬细胞T4和虹吸细胞0105phi7-2失活。对于细菌灭活和噬菌体不灭活，PrimeStore浓度存在安全边际。因此，期望具有普遍的适用性。随后的透析用于阻断对噬菌体的长期影响。尽管如此，应对每一种致病菌株/噬菌体进行比较试验。电镜切片显示失活改变的细菌细胞质和未解体的细菌包膜(鬼)。大肠杆菌的鬼影包括细胞质的重新排列和内毒素的释放。在随后的透析后，释放的内毒素的活性降低了99%，这也去除了PrimeStore成分。苏云金芽孢杆菌的鬼影包括细胞质内明显的相分离。设想的主要应用是用于治疗传染病的噬菌体的生物物理和其他筛选。
{"title":"Inactivating Host Bacteria for Characterization and Use of Phages","authors":"James P. Chambers, Elena T. Wright, Barbara Hunter, Philip Serwer","doi":"10.3390/biophysica3040038","DOIUrl":"https://doi.org/10.3390/biophysica3040038","url":null,"abstract":"Phage characterization for research and therapy can involve newly isolated phages propagated in pathogenic bacteria. If so, characterization requires safety-managing the bacteria. In the current study, we adapt a common and inexpensive reagent, PrimeStore (Longhorn Vaccines and Diagnostics, San Antonio, TX, USA), to safety-manage bacteria in 20 min by selectively inactivating the bacteria. No bacterial survivors are observed among >109 bacteria per ml for a representative of both Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Bacillus thuringiensis). This procedure causes no detected inactivation of podophage T3, myophage T4 and siphophage 0105phi7-2. Margins of safety for PrimeStore concentration exist for bacterial inactivation and phage non-inactivation. Thus, general applicability is expected. Subsequent dialysis is used to block long-term effects on phages. Nonetheless, comparable tests should be performed for each pathogenic bacterial strain/phage. Electron microscopy of thin sections reveals inactivation-altered bacterial cytoplasm and a non-disintegrated bacterial envelope (ghosts). Ghosting of E. coli includes re-arrangement of the cytoplasm and the release of endotoxin. The activity of the released endotoxin is >99% reduced after subsequent dialysis, which also removes PrimeStore components. Ghosting of B. thuringiensis includes apparent phase separation within the cytoplasm. The primary application envisaged is biophysical and other screening of phages for therapy of infectious disease.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135539152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-11DOI: 10.3390/biophysica3030037
Daniele Funaro
The deciphering of the genetic code takes place through the reading of the nitrogenous bases, which are four in number. In most cases, the bases are taken three by three, thus generating 64 possible combinations with repetition. Each combination (codon) allows for the synthesis of a specific amino acid. Since the latter are only 21 in number, the codon-amino acid conversion table shows a strong redundancy. Countless efforts have been made to understand the true encryption mechanism. Here, we want to add our version, which consists of associating a periodic sound based on three notes to each codon. RNA now becomes a dynamic object and not just a list of static instructions. In addition to a different interpretation of the genetic code, there is also a considerable reduction in redundancy, given that the number of periodic sounds that can be produced with three notes drops to 20 (with the addition of four pure frequencies). Finally, we discuss the possibility of how these sounds can be generated and travel inside the double helix, and possibly emitted as biophotons.
{"title":"A Dynamic Representation of mRNA Nucleotides Clarifies the Conundrum of Codon Redundancy","authors":"Daniele Funaro","doi":"10.3390/biophysica3030037","DOIUrl":"https://doi.org/10.3390/biophysica3030037","url":null,"abstract":"The deciphering of the genetic code takes place through the reading of the nitrogenous bases, which are four in number. In most cases, the bases are taken three by three, thus generating 64 possible combinations with repetition. Each combination (codon) allows for the synthesis of a specific amino acid. Since the latter are only 21 in number, the codon-amino acid conversion table shows a strong redundancy. Countless efforts have been made to understand the true encryption mechanism. Here, we want to add our version, which consists of associating a periodic sound based on three notes to each codon. RNA now becomes a dynamic object and not just a list of static instructions. In addition to a different interpretation of the genetic code, there is also a considerable reduction in redundancy, given that the number of periodic sounds that can be produced with three notes drops to 20 (with the addition of four pure frequencies). Finally, we discuss the possibility of how these sounds can be generated and travel inside the double helix, and possibly emitted as biophotons.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135981312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-05DOI: 10.3390/biophysica3030036
Marc Rico-Pasto, F. Ritort
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We consider cases where Brownian force fluctuations are large, masking the force rips and jumps characteristics of conformational transitions. We compare unfolding and folding data for DNA hairpin systems of loop sizes 4, 8, and 20 and the 110-amino acid protein barnase, finding conditions that facilitate the detection of folding events at low forces where the signal-to-noise ratio is low. In particular, we discuss the role of temperature as a useful parameter to improve the detection of folding transitions in entropically driven processes where folding forces are temperature independent. The force variance approach might be extended to detect the elusive intermediate states in RNA and protein folding.
{"title":"Detecting Molecular Folding from Noise Measurements","authors":"Marc Rico-Pasto, F. Ritort","doi":"10.3390/biophysica3030036","DOIUrl":"https://doi.org/10.3390/biophysica3030036","url":null,"abstract":"Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We consider cases where Brownian force fluctuations are large, masking the force rips and jumps characteristics of conformational transitions. We compare unfolding and folding data for DNA hairpin systems of loop sizes 4, 8, and 20 and the 110-amino acid protein barnase, finding conditions that facilitate the detection of folding events at low forces where the signal-to-noise ratio is low. In particular, we discuss the role of temperature as a useful parameter to improve the detection of folding transitions in entropically driven processes where folding forces are temperature independent. The force variance approach might be extended to detect the elusive intermediate states in RNA and protein folding.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42895803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-01DOI: 10.3390/biophysica3030035
M. Portaccio, B. Faramarzi, Maria Lepore
Infrared spectroscopy has emerged as a promising technique for studying the composition of biological samples like lipids that play important roles in cellular functions and are involved in various diseases. For this reason, lipids are a target of interest in many biomedical studies. The objective of the present study is to utilize Fourier-Transform Infrared (FT-IR) spectroscopy to examine the main lipid components of human cells (phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, C18 ceramide, sphingosine-1-phosphate, ceramide-1-phosphate, sphingomyelin, cholesterol, and triolein). FT-IR analysis on the previously mentioned lipid samples was performed in Attenuated Total Reflection (ATR) mode. The obtained spectra clearly evidence the contributions of the different functional groups that are present in the examined samples. Detailed assignments of spectral features were carried out in agreement with the literature. Similarities and differences among the different types of commercial lipid samples are evidenced and discussed, with particular attention to phospholipid and sphingolipid components. A quantitative analysis of phosphatidylinositol and sphingomyelin spectra using a ratiometric approach is reported. Moreover, a reconstruction procedure of FT-IR spectra of complex lipids useful for chemometrics applications is described. These representative examples of the potential use of the results of the present study can certainly contribute to a larger use of FT-IR spectroscopy in lipidomics.
{"title":"Probing Biochemical Differences in Lipid Components of Human Cells by Means of ATR-FTIR Spectroscopy","authors":"M. Portaccio, B. Faramarzi, Maria Lepore","doi":"10.3390/biophysica3030035","DOIUrl":"https://doi.org/10.3390/biophysica3030035","url":null,"abstract":"Infrared spectroscopy has emerged as a promising technique for studying the composition of biological samples like lipids that play important roles in cellular functions and are involved in various diseases. For this reason, lipids are a target of interest in many biomedical studies. The objective of the present study is to utilize Fourier-Transform Infrared (FT-IR) spectroscopy to examine the main lipid components of human cells (phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, C18 ceramide, sphingosine-1-phosphate, ceramide-1-phosphate, sphingomyelin, cholesterol, and triolein). FT-IR analysis on the previously mentioned lipid samples was performed in Attenuated Total Reflection (ATR) mode. The obtained spectra clearly evidence the contributions of the different functional groups that are present in the examined samples. Detailed assignments of spectral features were carried out in agreement with the literature. Similarities and differences among the different types of commercial lipid samples are evidenced and discussed, with particular attention to phospholipid and sphingolipid components. A quantitative analysis of phosphatidylinositol and sphingomyelin spectra using a ratiometric approach is reported. Moreover, a reconstruction procedure of FT-IR spectra of complex lipids useful for chemometrics applications is described. These representative examples of the potential use of the results of the present study can certainly contribute to a larger use of FT-IR spectroscopy in lipidomics.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48369377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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